Harley Quinn and Poison Ivy in the comics based on the DC Animated Universe - Ivy crashing the Joker and Harley's wedding leads Harley to dissolve their friendship once and for all. And in Gotham City Sirens #24 the Les Yay between Harley and Ivy is acknowledged and weaponized by Harley against Ivy when Ivy tries to "save" Harley from the Joker's influence. Near the end of the issue, Selina turns on Ivy as payback for one of Ivy's attacks in the past.
Green Lantern storyline Blackest Night sinks Kyle Rayner/Donna Troy, with both Kyle and Donna taking great pains to explain to Jade how utterly not interested in each other they are. It was case of Biting-the-Hand Humor since an editorial mandate around the time of Countdown to Final Crisis wanted them as a couple, sinking their ships at the time to make it happen.
The New Titans run plays with Terra II and Damage having feelings for each other, but sinks the ship by the end of the series with Damage feeling too put upon by Terra. Terra II also has feelings for Beast Boy, but he rejects her advances due to her resembling the original girl who betrayed him. Meanwhile, in the same run, any chances of Gar continuing to be paired off with his non-superhero girlfriend Jillian are sunk (and Jillian vanishs forever) after Terra II gets into a catfight with her and threatens her life to "stay away".
Wonder Girl and Superboy were the Official Couple throughout most of volume 3, but after Kon died for a time, Adam Beechen and Sean McKeever both had the intent of a Robin/Wonder Girl pairing... which wound up sunk itself and not lasting long. Kon then returned from the dead, but the Superboy/Wonder Girl ship wound up sunk when they broke up in J.T. Krul's run.
Robin (Tim Drake) and Secret from the Young Justice comic. Robin/Secret fans kept on sending letters to the editor about how they want them to end up together, despite the fact that Robin was never interested in any of his female team members and it looked like Secret's crush was unrequited. Finally, Peter David addressed the 'pairing' in issue #30, where Secret finds out about Robin's girlfriend Stephanie Brown, stalks her back to her house and attacks her in a jealous rage. After that, Robin kept being oblivious to Secret's feelings for him and she ended up being unstable and went over the dark side in the last few issues — which resulted in her attacking Stephanie for the second time.
During the New 52 reboot, DC tried to sink Superman and Lois Lane. It started off with pairing Lois with Jonathan Carroll or trying to set Clark up with her sister, and then Superman dating Wonder Woman. The torpedo, however seemed to have been launched when Lois reveals to the public that Clark is really Superman, but then they went and and fired a second torpedo towards Wonder Woman. Finally, DC threw their hands up and retconned the whole Superman/Wonder Woman's ship out during the DC Rebirth reboot, at the same time restoring the Clark/Lois' marriage.
Supergirl/Brainiac 5 ship was temporarily sunk in The '80s when Kara decides to quit the Legion and return to the 20th century. Although she promises to go back, she's killed in Crisis on Infinite Earths shortly after.
Formerly, The Unknown Supergirl sank Supergirl/Jerro. Jerro the Merboy -correctly- guesses Kara'll be too busy for romance after becoming a public hero, meaning he has lost his chance.
Batman and Catwoman despite having a year's worth of wedding bells were hit with a Shipping Torpedo by Tom King, as Selina fearing marrying Bruce would negate his role as Batman, leaves him at the altar. The fan response was "indisposed" to say the least, even the In-Universe justification of Rogues Gallery planning the Ship Sinking of Batman-Catwoman didn't mollify fans in the slightest. By the end of City of Bane, however, the ship rose from its grave.
Legion of Super-Heroes: Light Lass (Ayla Ranzz) and Timber Wolf (Brin Londo) were sunk during The Great Darkness Saga. Ayla gets sick of being a Legionnaire so she decides to quit the team. Brin is given the option to go with her, but he chooses not to. Ayla'd eventually rejoin the Legion, but she and Brin would never get back together.
